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Born in Vienna, his father, Leopold Breuer, taught religion in Vienna's Jewish community. Breuer's mother died when he was quite young, and he was raised by his maternal grandmother and educated by his father until the age of eight. He graduated from the Akademisches Gymnasium of Vienna in 1858 and then studied at the university for one year before enrolling in the medical school of the University of Vienna. He passed his medical exams in 1867 and went to work as assistant to the internistJohann Oppolzer at the university.

Breuer, working under Ewald Hering at the military medical school in Vienna, was the first to demonstrate the role of the vagus nerve in the reflex nature of respiration. This was a departure from previous physiological understanding, and changed the way scientists viewed the relationship of the lungs to the nervous system. The mechanism is now known as the Hering–Breuer reflex.[2]

Independent of each other[3] in 1873, Breuer and the physicist and mathematician Ernst Mach discovered how the sense of balance (i.e. the perception of the head’s imbalance) functions: that it is managed by information the brain receives from the movement of a fluid in the semicircular canals of the inner ear. That the sense of balance depends on the three semicircular canals was discovered in 1870 by the physiologist Friedrich Goltz, but Goltz did not discover how the balance-sensing apparatus functions.

Breuer is perhaps best known for his work in the 1880s with Anna O. (the pseudonym of Bertha Pappenheim), a woman suffering from "paralysis of her limbs, and anaesthesias, as well as disturbances of vision and speech."[4] Breuer observed that her symptoms reduced or disappeared after she described them to him. Anna O. humorously called this procedure chimney sweeping. She also coined the more serious appellation for this form of therapy, talking cure.[5] Breuer later referred to it as the “cathartic method”.

Breuer was then a mentor to the young Sigmund Freud, and had helped set him up in medical practice. Ernest Jones recalled, "Freud was greatly interested in hearing of the case of Anna O, which ... made a deep impression on him";[6] and in his 1909 Five Lectures on Psycho-Analysis, Freud generously pointed out, "I was a student and working for my final examinations at the time when ... Breuer, first (in 1880-2) made use of this procedure ... Never before had anyone removed a hysterical symptom by such a method."[7]

Freud and Breuer documented their discussions of Anna O. and other case studies in their 1895 book, Studies in Hysteria. These discussions of Breuer's treatment of Anna O. became "a formative basis of psychoanalytic practice, especially the importance of fantasies (in extreme cases, hallucinations), hysteria [...], and the concept and method of catharsis which were Breuer's major contributions."[8]Louis Breger has observed that in the Studies, "Freud is looking for a grand theory that will make him famous and, because of this, he is always fastening on what he thinks will be a single cause of hysteria, such as sexual conflict...Breuer, on the other hand, writes about the many factors that produce symptoms, including traumas of a variety of kinds. He also gives others, such as Pierre Janet, credit and argues for “eclecticism”; he is open to many different ways of understanding and treating hysteria."[9]

The two men became increasingly estranged. From a Freudian standpoint, "while Breuer, with his intelligent and amorous patient Anna O., had unwittingly laid the groundwork for psychoanalysis, it was Freud who drew the consequences from Breuer's case."[10] However, Breger notes that Breuer, while he valued Freud’s contributions, didn’t agree that sexual issues were the only cause of neurotic symptoms; he wrote in a 1907 letter to a colleague that “Freud is a man given to absolute and exclusive formulations: this is a psychical need which, in my opinion, leads to excessive generalization.” Freud later turned on Breuer, no longer giving him credit and helping spread a rumour that Breuer had not been able to handle erotic attention from Anna O. and had abandoned her case, though research indicates this never happened and Breuer remained involved with her case for several years while she remained unwell.[9]

Breuer married Mathilde Altmann in 1868, and they had five children. His daughter Dora later committed suicide rather than be deported by the Nazis. Another one of his daughters, Margarete Schiff, perished in Theresienstadt on September 9, 1942. Breuer's granddaughter, Hanna Schiff, died while imprisoned by the Nazis.

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